Consumption of N2O by Flavobacterium azooxidireducens sp. nov. Isolated from Decomposing Leaf Litter of Phragmites australis (Cav.)

Abstract

Microorganisms acting as sinks for the greenhouse gas nitrous oxide (N₂O) are gaining increasing attention in the development of strategies to control N₂O emissions. Non-denitrifying N₂O reducers are of particular interest because they can provide a real sink without contributing to N₂O release. The bacterial strain under investigation (IGB 4-14^T), isolated in a mesocosm experiment to study the litter decomposition of Phragmites australis (Cav.), is such an organism. It carries only a nos gene cluster with the sec-dependent Clade II nosZ and is able to consume significant amounts of N₂O under anoxic conditions. However, consumption activity is considerably affected by the O₂ level. The reduction of N₂O was not associated with cell growth, suggesting that no energy is conserved by anaerobic respiration. Therefore, the N₂O consumption of strain IGB 4-14^T rather serves as an electron sink for metabolism to sustain viability during transient anoxia and/or to detoxify high N₂O concentrations. Phylogenetic analysis of 16S rRNA gene similarity revealed that the strain belongs to the genus Flavobacterium. It shares a high similarity in the nos gene cluster composition and the amino acid similarity of the nosZ gene with various type strains of the genus. However, phylogenomic analysis and comparison of overall genome relatedness indices clearly demonstrated a novel species status of strain IGB 4-14^T, with Flavobacterium lacus being the most closely related species. Various phenotypic differences supported a demarcation from this species. Based on these results, we proposed a novel species Flavobacterium azooxidireducens sp. nov. (type strain IGB 4-14^T = LMG 29709^T = DSM 103580^T).

Keywords: Clade II nosZ; Flavobacterium azooxidireducens sp. nov.; nitrous oxide reduction; non-denitrifier; phylogenomic analysis.

Figure 4

(a) Cumulative net N₂O reduction; (b) cumulative net CO₂ production; and (c) O₂ depletion by strain IGB 4-14^T under anoxic, microoxic (4% O₂) and oxic (20% O₂) conditions. The plotted values are averages of six repetitions, corrected by the average of three controls. Error bars represent the standard deviations. Different letters indicate significant differences (p < 0.05).

Figure 1

Maximum-likelihood tree of the 16S rRNA gene sequences showing the position of strain IGB 4-14^T among phylogenetically related species of genus Flavobacterium. Filled circles indicate branches of the tree that were also obtained using neighbour-joining algorithm. The sequence GU166749 of Lutibacter flavus IMCC1507^T was used as an outgroup. Numbers at branch nodes refer to bootstrap values ≥70%. Bar: substitutions per nucleotide site. Accession numbers (NCBI or IMG database) are indicated in brackets.

Figure 2

Phylogenomic tree showing the position of strain IGB 4-14^T within the genus Flavobacterium. The strain Lutibacter flavus IMCC1507^T was used as an outgroup. The maximum-likelihood tree is based on concatenated 120 core marker proteins. Numbers at branch nodes refer to bootstrap values >70%. Bar: amino acid substitutions per position. Assembly accession numbers are indicated in brackets.

Figure 3

Maximum-Likelihood based phylogeny of NosZ amino-acid sequences showing the position of strain IGB 4-14^T among a selection of type strains of Flavobacterium species and reference strains according to Sanford, et al. [4]. The scale bar indicates the number of amino acid substitutions per site.